--- /dev/null
+---
+channel: release
+version: 2.8.0b1
+date: 2014-01-30
+---
+
+## New Features
+
+- Trusted certificates for JalviewLite applet and Jalview Desktop application<br/>
+Certificate was donated by [Certum](https://www.certum.eu) to the Jalview open source project).
+- Jalview SRS links replaced by UniProt and EBI-search
+- Output in Stockholm format
+- Allow import of data from gzipped files
+- Export/import group and sequence associated line graph thresholds
+- Nucleotide substitution matrix that supports RNA and ambiguity codes
+- Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
+- Groovy scripting for headless Jalview operation
+
+
+### Other improvements
+- Upgrade desktop installer to InstallAnywhere 2013
+- COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows
+- Support '' style escaping of quotes in Newick files
+- Group options for JABAWS service by command line name
+- Empty tooltip shown for JABA service options with a link but no description
+- Select primary source when selecting authority in database fetcher GUI
+- Add .mfa to FASTA file extensions recognised by Jalview
+- Annotation label tooltip text wrap
+
+
+## Issues Resolved
+
+- Slow scrolling when lots of annotation rows are displayed
+- Lots of NPE (and slowness) after creating RNA secondary structure annotation line
+- Sequence database accessions not imported when fetching alignments from Rfam
+- Incorrect SHMR submission for sequences with identical IDs
+- View all structures does not always superpose structures
+- Option widgets in service parameters not updated to reflect user or preset settings
+- Null pointer exceptions for some services without presets or adjustable parameters
+- Discover PDB IDs entry in structure menu doesn't discover PDB xRefs
+- Exception encountered while trying to retrieve features with DAS
+- Lowest value in annotation row isn't coloured when colour by annotation (per sequence) is coloured
+- Keyboard mode P jumps to start of gapped region when residue follows a gap
+- Jalview appears to hang importing an alignment with Wrap as default or after enabling Wrap
+- 'Right click to add annotations' message shown in wrap mode when no annotations present
+- Disorder predictions fail with NPE if no automatic annotation already exists on alignment
+- oninit javascript function should be called after initialisation completes
+- Remove redundancy after disorder prediction corrupts alignment window display
+- Example annotation file in documentation is invalid
+- Grouped line graph annotation rows are not exported to annotation file
+- Multi-harmony analysis cannot be run when only two groups created
+- Cannot create multiple groups of line graphs with several 'combine' statements in annotation file
+- Pressing return several times causes Number Format exceptions in keyboard mode
+- Multi-harmony (SHMMR) method doesn't submit correct partitions for input data
+- Translation from DNA to Amino Acids fails
+- Jalview fail to load newick tree with quoted label
+- --headless flag isn't understood
+- ClassCastException when generating EPS in headless mode
+- Adjusting sequence-associated shading threshold only changes one row's threshold
+- Preferences and Feature settings panel panel doesn't open
+- hide consensus histogram also hides conservation and quality histograms
git://source.jalview.org / jalview.git / blobdiff